KODAMA (version 1.6)

k.test: K-Test of Statistical Association

Description

This function performs a permutation test using PLS to assess association between the KODAMA output and any additional related parameters such as clinical metadata.

Usage

k.test(data, labels, n = 100)

Arguments

data

a matrix.

labels

a classification vector.

n

number of iterations of the permutation test.

Value

The p-value of the test.

References

Cacciatore S, Luchinat C, Tenori L Knowledge discovery by accuracy maximization. Proc Natl Acad Sci U S A 2014;111(14):5117-22. doi: 10.1073/pnas.1220873111. Link

Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA KODAMA: an updated R package for knowledge discovery and data mining. Bioinformatics 2017;33(4):621-623. doi: 10.1093/bioinformatics/btw705. Link

See Also

KODAMA

Examples

# NOT RUN {
 data(iris)
 data=iris[,-5]
 labels=iris[,5]
 kk=KODAMA(data,FUN="PLS-DA")
 kkplot=kk$pp
 k1=k.test(kkplot,labels)
 print(k1)
 k2=k.test(kkplot,sample(labels))
 print(k2)
# }